Maintained by Robin Tecon, microbiologist and postdoctoral researcher at the Swiss Federal Institute of Technology Zürich. This blog is about bacteria (and other microbes) and the scientists who study them.

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Sunday, September 16, 2012

The Logic of Chance by Eugene Koonin

About fifteen years ago, a revolution started in the
biological sciences, which goes by the name whole
genome sequencing. I don’t have memories of the announcement of the first
bacterial genome in 1995 (I was in high school and not really following biology
news…), but at the time of the human genome project I was a biology student at
the University and I remember very well when the paper describing the human
genome came out in 2001 (we had to read it in class!).

Until recently, my feeling about whole genome sequencing was
that it was a technical revolution, not a conceptual one. After all, I thought,
the sequence information revolution already took place in the seventies, when
Carl Woese pioneered the use of 16S ribosomal RNA to construct phylogeny.

I revised this feeling, thanks in part to the excellent book
of Eugene Koonin, The Logic of Chance
(2011)—subtitled
the nature and origin of biological
evolution—and published by Financial Times Press (yes, they do have a
science catalog!).

I had heard
of Eugene Koonin here or there, without really fixing the name in my mind, but
recently a friend mentioned him as an important scientist in comparative
genomics, so I decided to look for his work. Koonin is senior investigator at
the NCBI—and
with a couple of hundreds of scientific publications, he’s quite a big shot in
the field!

The title The Logic of Chance
invokes both Chance and Necessity by
Jacques Monod and The Logic of Life by
François Jacob, two great scientists to whom Koonin’s book often refers. This
is his first book, and he obviously put a lot of effort in it. Interestingly,
it’s the recent wave of popularized writings in theoretical physics (Hawking,
Weinberg, etc.) that the author wanted to emulate in his own field of evolutionary biology.

This is a big book (516 pages) containing many graphs and
informative “boxes”, something more common in journal reviews and textbooks. In
that respect, Koonin perhaps hesitated between an essay accessible to a large audience
and a treatise for the specialists. Fortunately, each chapter finishes with a
synopsis to make sure the key ideas are understood. Despite this, I believe the
layman reader would have a hard time.

The book covers many topics, and I skipped some parts in my
reading, but what I would like to stress is that Koonin really gives a detailed
and current view of the research on evolution
based on comparative genomics: Thus, a majority of the journal references were
written within the past five years! As I see it, the book discusses two major topics: One, historical,
deals with the living organisms and their origins; the other, mechanistic,
deals with what drives evolution. The two are intertwined in different chapters
throughout the book.

After a welcomed refresher on evolutionary biology from
Darwin to the modern synthesis and up to the genomics era, Koonin rapidly comes
to the crux of the matter, which is comparative genomics.

[I was first
introduced to it as a student, through the comparative genometrics group at the University of Lausanne (the group does not exist anymore in Lausanne, but its former members are active in other universities). The analysis of whole bacterial genomes revealed lots of interesting
peculiarities in the structure of the DNA sequence, but at that time I failed
to seize the implications for the broader picture, that is for evolution as a
whole.]

Histories of genes and species

The first important observation stemming from comparative
genomics is that individual genes are much more conserved among different
species that the whole genome architecture. (This supports the common view in
which selection operates on genes, whereas individuals are only the vehicle of
these genes). For the same reason, it is very difficult (maybe even impossible)
to construct phylogenetic trees at the species level, because multiple trees
may disagree depending on what gene(s) is concerned.

At the prokaryotic level,
the tree of life model, which deals
with species, is undermined by the high prevalence of horizontal gene transfer
(HGT). In replacement, Koonin emphasizes the idea of a forest of life, that is, a collection of trees made for all genes (Koonin & Wolf, 2009). This, however, is different in eukaryotes. With the
exception of the initial endosymbiosis events, HGT is not dominant in
eukaryotes (sex replaced it to produce genetic exchange!). Hence, tree-like
representations work much better for eukaryotes than for prokaryotes. But this doesn’t
help solving a major conundrum: How did the first eukaryote evolve? Apparently,
the details of this event are far from being settled…

On top of prokaryotes and eukaryotes, Koonin reminds us of
the importance of viruses (a whole chapter is dedicated to the “virus world”). Koonin
goes as far as defining two “empires” of life: viruses and selfish genetic elements
on the one hand, and cellular organisms on the other hand. As the author notes,
viruses are, at least in terms of mere numbers, the dominant biological
entities on Earth!